WASHINGTON — The Education Department’s Office for Civil Rights has begun dismissing hundreds of civil rights complaints under a new protocol that allows investigators to disregard cases that are part of serial filings or that they consider burdensome to the office.

Department officials said the new policy targeted advocates who flooded the office with thousands of complaints for similar violations, jamming its investigation pipeline with cases that could be resolved without exhausting staff and resources. But civil rights advocates worry that the office’s rejection of legitimate claims is the most obvious example to date of its diminishing role in enforcing civil rights laws in the nation’s schools.

The goal of the new manual, which took effect last month, is to help the office better manage its docket, investigations and resolutions, she said.

Among the changes implemented immediately is a provision that allows the Office for Civil Rights to dismiss cases that reflect “a pattern of complaints previously filed with O.C.R. by an individual or a group against multiple recipients,” or complaints “filed for the first time against multiple recipients that” place “an unreasonable burden on O.C.R.’s resources.”

So far, the provision has resulted in the dismissal of more than 500 disability rights complaints.

Catherine E. Lhamon, who led the Office for Civil Rights under the Obama administration, said the new provision undermined the mission of the office. Unlike the Justice Department, the Education Department cannot pick and choose the cases it pursues. If the office has evidence that the law has been violated, it must open a case.

“The thing that scares me is when they get to say ‘we won’t open some cases because it’s too much for us,’ or ‘we don’t like the complainant,’ or ‘it’s not our week to work on that,’ you start to change the character of the office,” Ms. Lhamon said.

But Debora L. Osgood, a lawyer who worked for 25 years at the Office for Civil Rights and now consults with and represents schools on civil rights matters, praised the change.

She said the provision showed that the agency was “essentially taking the reins back for control of its complaint docket.”

Ms. Osgood said that in her experience, one person could clog the pipeline in each of the agency’s 12 regional offices, limiting investigators’ ability to respond to other complaints. It often frustrated investigators who prided themselves on being able to resolve complaints promptly, she said.

“In effect, it turned over the decision-making about how the agency would use many of its resources to a single individual, rather than to agency officials and staff charged with the responsibility for implementing the agency’s stated mission,” she said.

According to the Education Department, 41 percent of the 16,720 complaints filed in the 2016 fiscal year came from three people. The next year, of the 12,837 total cases, 23 percent of them did.

The department calls the complainants “frequent fliers.”

Marcie Lipsitt is proud to be one of them.

In the last two years, Ms. Lipsitt, a disability rights advocate in Michigan, has filed more than 2,400 complaints with the office against schools, departments of education, colleges and universities, libraries and other educational institutions across the country that have websites that people who are deaf or blind or who struggle with fine motor skills cannot navigate.

“No one even knew about this issue until I started filing,” Ms. Lipsitt said. “I didn’t want to get anybody in trouble. I just wanted to raise awareness.”

She has secured more than 1,000 agreements with institutions that committed to bringing their websites into compliance with the Rehabilitation Act of 1973, which prohibits discrimination against people with disabilities and requires that electronic and information technologies be accessible to them.

In recent weeks, Ms. Lipsitt said, she has received notice that more than 500 cases, including active and open investigations, were dismissed. Each letter cited the new provision as the reason. The department will instead work with colleges on complying with web accessibility laws.

“But I won’t stop,” Ms. Lipsitt vowed, “because if I do, the story goes away.”

The new manual also eliminates an appeals process for Office for Civil Rights decisions — department officials said it usually resulted in the same outcome — and says complaints can no longer be filed on the basis of journal articles and news media reports.

The manual also drops all mention of investigators’ looking into “systemic issues.” However, the department said that the new provision would not apply to class-action-like complaints filed by groups.

The changes worry civil rights groups, which point out that Education Secretary Betsy DeVos has already rescinded guidances meant to protect students against sexual assaults on campuses and black and transgender students against bias.

Neena Chaudhry, associate general counsel and senior adviser of education at the National Women’s Law Center, said that by filing dozens of complaints in recent decades, the group has been able to secure equal scholarship money and increased sports opportunities for female athletes. Now, as the organization shifts its focus to sexual assault, the department may prove less responsive.

Rachel M. Kleinman, senior counsel at the NAACP Legal Defense Fund, said that the new manual was “yet another avenue for O.C.R. to not seriously investigate systemic race discrimination.”

The group has filed complaints on behalf of large groups of black students it believes were being disproportionately affected by law enforcement policies. Already, one case has been closed by the DeVos administration, and the department declined to conduct a broader analysis.

“They seem to be closing all of the pathways for students to have their rights enforced by the federal government,” Ms. Kleinman said.

Ms. DeVos’s Office for Civil Rights has maintained that it wants to be more efficient and effective than it was under the Obama administration, which was known for its aggressive enforcement and broad investigations but was also accused of being overzealous and leaving cases languishing for years.

Ms. Osgood said such changes would be welcomed by the colleges and universities that she assists with federal civil rights investigations.

She said the changes showed that the department was willing to work with schools in a “more reasonable, more nimble and more expeditious manner.”

The department did not say how its investigators would determine that a case would place an “unreasonable burden” on its resources. However, just weeks after the new manual took effect, Congress allocated $8.5 million more in funding to the Office for Civil Rights, which Ms. DeVos had sought to cut, in order for the office to manage its caseload.

Ms. Lhamon said that, in her time in the office, she sought out ways to manage large volumes of cases that stemmed from one complainant, and she acknowledged that her office struggled with timely responses. But she said she could not come up with any measure that would not shortchange an investigation.

“There’s not a limitation on justice, and there’s not a limitation on how we perceive injustice,” Ms. Lhamon said. “To say you’ve reached your quota is to say that there’s somehow a cap on the number of children who might be harmed.”

A version of this article appears in print on April 20, 2018, on Page A14 of the New York edition with the headline: Education Dept. Aims for Efficiency by Dismissing Rights Cases. Order Reprints | Today’s Paper | Subscribe